The histone N-terminal tails are subjected to multiple covalent modifications that affect chromatin structure and consequently transcription. One of the best-characterized modifications is acetylation, which is controlled by both histone acetyltransferases (HATs) and deacetylases (HDACs) suggesting that acetylation regulation is a dynamic process (Kouzarides, 2000). More recently, histone methylation has also emerged as a form of posttranslational modification that significantly impacts chromatin structure (Rice and Allis, 2001; Zhang and Reinberg, 2001). Unlike histone acetylation, which takes places only on lysine (K), methylation occurs on both lysine and arginine (R). While acetylation is generally correlated with active transcription (Roth et al., 2001), histone methylation is linked to both transcriptional activation and repression (Zhang and Reinberg, 2001). For instance, histone H3 K9 (H3-K9) methylation is associated with heterochromatin formation (Nakayama et al., 2001; Peters et al., 2002; Rea et al., 2000) and also euchromatic gene repression (Nielsen et al., 2001; Shi et al., 2003). In the case of heterochromatin assembly, H3-K9 is first methylated by Suv39H, and the methylated K9 is then recognized and bound by the chromodomain protein HP1 (Bannister et al., 2001; Lachner et al., 2001; Nakayama et al., 2001). The Suv39H-HP1 methylation system is proposed to be responsible for heterochromatin propagation. In contrast, methylation of histone H3 K4 (H3-K4) is linked to active transcription (Liang et al., 2004; Litt et al., 2001; Noma et al., 2001; Santos-Rosa et al., 2002; Schneider et al., 2004), as is methylation of arginine residues of histone H3 and H4 (Zhang and Reinberg, 2001). Mechanisms that underlie methylation-dependent transcriptional activation are not completely understood, although H3-K4-specific methylases have recently been shown to associate with RNA polymerase II (Hamamoto et al., 2004; Ng et al., 2003b).
While histone acetylation is dynamically regulated by HATs and HDACs, histone methylation has been considered a “permanent” modification. At least two models are currently being considered to explain the turnover of methyl groups on histones. The first one suggests that a cell may remove histone methylation by clipping the histone tail (Allis et al., 1980) or by replacing the methylated histone with a variant histone in the case of methyl group turnover at H3-K9 (Ahmad and Henikoff, 2002; Briggs et al., 2001; Johnson et al., 2004). However, this mechanism would not allow for dynamic regulation of histone methylation and the plasticity that may be essential for gene transcription regulation in some biological processes. The second model proposes the existence of histone demethylases that function to remove the methyl groups from lysine and arginine, which would make dynamic regulation possible. Recently, a human peptidyl arginine deiminase, PAD14/PAD4, has been shown to antagonize methylation on the arginine residues by converting arginine to citrulline, (Cuthbert et al., 2004; Wang et al., 2004). PAD14/PAD4 catalyzes the deimination reaction irrespective of whether the arginine residue is methylated or not. These findings suggest that histone methylation can be dynamically regulated through the opposing actions of histone methylases and enzymes such as PAD14/PAD4. However, since PAD14/PAD4 catalyzes deimination but not demethylation, it remains unclear whether bona fide histone demethylases exist. The search for histone demethylases began in the 1960s when Paik and colleagues first reported an enzyme that can demethylate free mono- and di-N-methyllysine (Kim et al., 1964). Subsequently, the same investigators partially purified an activity that can demethylate histones (Paik and Kim, 1973; Paik and Kim, 1974). These early studies suggested the possibility that histone demethylases may exist but the molecular identity of these putative histone demethylases have remained elusive for the past four decades.
Classical amine oxidases play important roles in metabolism and their substrates range from small molecules (e.g., spermine and spermidine) to proteins. More recently, amine oxidases have also been proposed to function as histone demethylases via an oxidation reaction that removes methyl groups from lysine or arginine residues of histones (Bannister et al., 2002). KIAA0601 encodes a protein that shares significant sequence homology with FAD-dependent amine oxidases (Humphrey et al., 2001; Shi et al., 2003). We identified KIAA0601/NPAO as a component of the CtBP co-repressor complex (Shi et al., 2003), and it has also been found in a number of other co-repressor complexes, including NRD (Tong et al., 1998), Co-REST (You et al., 2001), and subsets of the HDAC complexes (Hakimi et al., 2002; Hakimi et al., 2003; Humphrey et al., 2001). Recent studies of the C. elegans homolog, SPR-5, provided genetic evidence for a role in transcriptional repression (Eimer et al., 2003; Jarriault and Greenwald, 2002). However, its exact role in transcriptional regulation has been unclear.
There is a continuing need in the art to identify the components of the transcription regulatory system so that they can be manipulated to treat diseases that involve aberrations of the system.